The Big Guy is decommissioned in favor of Quark Industries' newest creation, Rusty the Boy Robot. But when an alien Annihilator threatens to destroy New Tronic City, it's clear that Rusty is not quite ready for prime time. The Big Guy is reassembled and joins the fight along with Rusty. General Thorton orders that the temporary alliance become a permanent partnership.
Dr. Gilder, the Legion Ex Machina's mole within Quark, has developed a personal grudge against Donovan, so he takes control of a prototype and tries to assassinate him. Donovan is taken to the S.S. Dark Horse for his own safety. Gilder then hacks into Rusty, gives him a ""big gun"", and sets out to destroy Donovan.
Dr. Slate, Big Guy and Rusty find out that the Legion Ex Machina's mysterious ""final assembly"" is taking place in a network of underground tunnels. When Big Guy and Rusty find the tunnels, they derail a robotic train. Inside the massive train's cargo hold is a gigantic hand that boasts a built-in high-tech cannon. With their plan uncovered, the Legion Ex Machina members decide to activate their latest creation ahead of schedule and missing a hand.
When Quark's Dr. Kirby disappears after an experiment with his Quantum Machine goes awry, a hostile monster emerges and goes on a rampage, apparently having destroyed the doctor. Back at Quark, Rusty discovers a previous ""boy robot"" prototype. Hoping for a new friend, Rusty reassembles the robot, who he names ""Earl."" But Earl's relentlessly aggressive programming turns him against the heroes.
Donovan unveils Quark's latest prototype: tiny liquid metal robots called Nurds that repair and upgrade any technology they come in contact with. When Big Guy becomes infested by the Nurds, they repair its original artificial intelligence circuitry, making Big Guy a fully functioning robot, which removes Dwayne from the pilot's seat. But shortly after the new Big Guy successfully completes his first mission, things go awry.
Being powered up for six months, Rusty has not grown an inch. Frustrated that he will never be as big as The Big Guy, he connects his robot head on the powerful robot body of Quark's T-7000 Prototype. But he learns there's more to crime-fighting than just being big when a gang of exosuit-wearing chopshoppers (Gage, Big Rig, and Cargo) lure him into an ambush.
While trying to keep the Legion Ex Machina's newest robot from absconding with Quarks' new anti-neutrinos, Rusty plugs into the bot's software to learn the Legion's secrets. #4 counters Rusty's hack by engaging in a mental tug of war. A power surge switches personality traits between the two robots. Rusty starts building a doomsday machine while #4 plays video games.